Gene copy number variants (CNVs), which consist of gene deletions and amplifications contribute to the great diversity in the Plasmodium falciparum genome. CNVs may influence the expression of genes and hence may affect important parasite phenotypes such as virulence, drug resistance, persistence and transmissibility. The hypothesis underlying the studies in this thesis is that CNVs may be important for adaptation of the parasite to its variable environments. To investigate this hypothesis, a population wide survey of CNVs in 183 fresh field isolates from four populations with different transmission intensities was conducted. To detect CNVs, comparative genome hybridization was performed using a 70mer microarray. This is the first large scale survey for CNVs in natural populations of parasites. A total of 98 different CNVs, consisting of 225 genes, were identified. Various systematic aspects that could affect detection of CNVs were explored and the population of origin of the isolate was found to be the only factor that affects CNV detection. Some of these CNVs showed high differentiation in frequency between populations suggestive of the action of directional selection. Other CNVs showed no or low differentiation in frequencies between populations, indicative of action of neutral evolutionary processes. Validation of the CNVs identified using microarrays was done using whole genome sequencing. Very low concordance was observed between the CNVs identified by the two technologies. These differences may be attributed to technical and analytic differences between the two technologies. Furthermore, the effect of CNVs on gene expression levels was analysed. A number of CNVs were found to be significantly associated (positively or negatively) with the expression levels of genes located inside and also outside the CNVs
